RetrogeneDB ID: | retro_itri_1824 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393911.1:175059..175589(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM38B | ||
| Ensembl ID: | ENSSTOG00000003014 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 38B [Source:HGNC Symbol;Acc:25535] |
Retrocopy-Parental alignment summary:
>retro_itri_1824
ATGGACTCTCCATGGGAAAAGCTGGCATTGGCCTTCTCCTGCACGTCCATGTTCCCCTTTTTTTTGACATCACCCACATC
TGTTGTCTGTGATGGCCTTGAAGCATCAGCTGGTAGGAGTGGAAGGAGCATGGAAGAATCCTGTTTCAAGCTGGTCTACT
GCTTTGATCCCTGATTTGGTGGAGAAATTTTAACATGTGTACTGCTTGAAGAGCCTCCACTGAGGTTTCTTGCAAACCCC
ATTAATATTTTACTGGCATCTTCAATCTGGTATATTACATATATTTTTGCCCATGGGACCTAAATTCCCAGGACTATTCA
TTCTTATCCGCTCAACTTCTGGCTGTGGGAATGAAGGAGTGATAAGAATTTGGAAATTAGAAGGTGGAATCACACATGCT
AATAGCTATTACAAAAATGGCTGGCCAGTCATGATAGCTATTGGATGGGCCCAAGGTGCAGCTGGTATCACTATCATGAA
TTTTGAACAGTTGGTAAAGGAGATTGGAAACCAGAGATGATGAATGGCTT
ORF - retro_itri_1824 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.57 % |
| Parental protein coverage: | 60.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | MDSSWEDLTLAFSRTSMFPFFDIA-HYLVSVMALKHRPGAVEGAWKNPFSSWFTAMLHC-FGGGILSCIL |
| MDS.WE.L.LAFS.TSMFP........L.SVMALKH....VEGAWKNP.SSW.TA.....FGG.IL.C.L | |
| Retrocopy | MDSPWEKLALAFSCTSMFPXXXTS>PHLLSVMALKHQLVGVEGAWKNPVSSWSTALIPD<FGGEILTCVL |
| Parental | LAEPPLRFFANHTNVLLASSIWYIIF-FCP-WDLISQGYSFLPVQLLAAGMKE-VTRTWKIIGGITHANS |
| L.EPPLRF.AN..N.LLASSIWYI...F.P.WDL.SQ.YSFL..QLLA.GMKE.V.R.WK..GGITHANS | |
| Retrocopy | LEEPPLRFLANPINILLASSIWYITY>FLP>WDLNSQDYSFLSAQLLAVGMKE<VIRIWKLEGGITHANS |
| Parental | YYKNGWLVMIAIGWAQGAGGIIITNFEQLL-KGDWKPE-GNEWL |
| YYKNGW.VMIAIGWAQGA.GI.I.NFEQL..KGDWKPE...EWL | |
| Retrocopy | YYKNGWPVMIAIGWAQGAAGITIMNFEQLV<KGDWKPE<DDEWL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_1824 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1824 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000002467 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000003014 | 7 retrocopies |
retro_itri_1553, retro_itri_1708, retro_itri_1789, retro_itri_1823, retro_itri_1824 , retro_itri_1826, retro_itri_1845,
|